def kde_plot_1d(ax, data, *args, **kwargs): """Plot a 1d marginalised distribution. This functions as a wrapper around matplotlib.axes.Axes.plot, with a kernel density estimation computation provided by scipy.stats.gaussian_kde in between. All remaining keyword arguments are passed onwards. Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on. data: numpy.array Samples to generate kernel density estimator. weights: numpy.array, optional Sample weights. ncompress: int, optional Degree of compression. Default 1000 xmin, xmax: float lower/upper prior bound. optional, default None Returns ------- lines: matplotlib.lines.Line2D A list of line objects representing the plotted data (same as matplotlib matplotlib.axes.Axes.plot command) """ if len(data) == 0: return numpy.zeros(0), numpy.zeros(0) if data.max() - data.min() <= 0: return xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) weights = kwargs.pop('weights', None) ncompress = kwargs.pop('ncompress', 1000) x, w = sample_compression_1d(data, weights, ncompress) kde = gaussian_kde(x, weights=w) p = kde(x) p /= p.max() i = ((x < quantile(x, 0.999, w)) & (x > quantile(x, 0.001, w))) | (p > 0.1) if xmin is not None: i = i & (x > xmin) if xmax is not None: i = i & (x < xmax) sigma = numpy.sqrt(kde.covariance[0, 0]) pp = cut_and_normalise_gaussian(x[i], p[i], sigma, xmin, xmax) pp /= pp.max() ans = ax.plot(x[i], pp, *args, **kwargs) ax.set_xlim(*check_bounds(x[i], xmin, xmax), auto=True) return ans
def fastkde_plot_1d(ax, data, *args, **kwargs): """Plot a 1d marginalised distribution. This functions as a wrapper around matplotlib.axes.Axes.plot, with a kernel density estimation computation provided by the package fastkde in between. All remaining keyword arguments are passed onwards. Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on data: np.array Uniformly weighted samples to generate kernel density estimator. xmin, xmax: float lower/upper prior bound optional, default None Returns ------- lines: matplotlib.lines.Line2D A list of line objects representing the plotted data (same as matplotlib matplotlib.axes.Axes.plot command) """ if len(data) == 0: return np.zeros(0), np.zeros(0) if data.max() - data.min() <= 0: return xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) cmap = kwargs.pop('cmap', None) color = kwargs.pop('color', (next(ax._get_lines.prop_cycler)['color'] if cmap is None else cmap(0.68))) q = kwargs.pop('q', '5sigma') q = quantile_plot_interval(q=q) try: x, p = fastkde_1d(data, xmin, xmax) except NameError: raise ImportError("You need to install fastkde to use fastkde") p /= p.max() i = ((x > quantile(x, q[0], p)) & (x < quantile(x, q[1], p))) ans = ax.plot(x[i], p[i], color=color, *args, **kwargs) ax.set_xlim(*check_bounds(x[i], xmin, xmax), auto=True) return ans
def hist_plot_1d(ax, data, *args, **kwargs): """Plot a 1d histogram. This functions is a wrapper around matplotlib.axes.Axes.hist. All remaining keyword arguments are passed onwards. Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on data: numpy.array Samples to generate histogram from weights: numpy.array, optional Sample weights. xmin, xmax: float lower/upper prior bound. optional, default data.min() and data.max() cannot be None (reverts to default in that case) Returns ------- patches : list or list of lists Silent list of individual patches used to create the histogram or list of such list if multiple input datasets. Other Parameters ---------------- **kwargs : `~matplotlib.axes.Axes.hist` properties """ if data.max() - data.min() <= 0: return xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) plotter = kwargs.pop('plotter', '') weights = kwargs.pop('weights', None) if xmin is None: xmin = quantile(data, 0.01, weights) if xmax is None: xmax = quantile(data, 0.99, weights) histtype = kwargs.pop('histtype', 'bar') if plotter == 'astropyhist': try: h, edges, bars = hist(data, ax=ax, range=(xmin, xmax), histtype=histtype, *args, **kwargs) except NameError: raise ImportError("You need to install astropy to use astropyhist") else: h, edges, bars = ax.hist(data, range=(xmin, xmax), histtype=histtype, weights=weights, *args, **kwargs) if histtype == 'bar': for b in bars: b.set_height(b.get_height() / h.max()) elif histtype == 'step' or histtype == 'stepfilled': trans = Affine2D().scale(sx=1, sy=1. / h.max()) + ax.transData bars[0].set_transform(trans) ax.set_xlim(*check_bounds(edges, xmin, xmax), auto=True) ax.set_ylim(0, 1.1) return bars
def hist_plot_2d(ax, data_x, data_y, *args, **kwargs): """Plot a 2d marginalised distribution as a histogram. This functions as a wrapper around matplotlib.axes.Axes.hist2d Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on data_x, data_y: np.array x and y coordinates of uniformly weighted samples to generate kernel density estimator. xmin, xmax, ymin, ymax: float lower/upper prior bounds in x/y coordinates optional, default None levels: list Shade iso-probability contours containing these levels of probability mass. If None defaults to usual matplotlib.axes.Axes.hist2d colouring. optional, default None Returns ------- c: matplotlib.collections.QuadMesh A set of colors """ xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) ymin = kwargs.pop('ymin', None) ymax = kwargs.pop('ymax', None) vmin = kwargs.pop('vmin', 0) label = kwargs.pop('label', None) levels = kwargs.pop('levels', None) color = kwargs.pop('color', next(ax._get_lines.prop_cycler)['color']) weights = kwargs.pop('weights', None) if xmin is None or not np.isfinite(xmin): xmin = quantile(data_x, 0.01, weights) if xmax is None or not np.isfinite(xmax): xmax = quantile(data_x, 0.99, weights) if ymin is None or not np.isfinite(ymin): ymin = quantile(data_y, 0.01, weights) if ymax is None or not np.isfinite(ymax): ymax = quantile(data_y, 0.99, weights) rge = kwargs.pop('range', ((xmin, xmax), (ymin, ymax))) if len(data_x) == 0 or len(data_y) == 0: return np.zeros(0), np.zeros(0), np.zeros((0, 0)) cmap = kwargs.pop('cmap', basic_cmap(color)) if levels is None: pdf, x, y, image = ax.hist2d(data_x, data_y, weights=weights, cmap=cmap, range=rge, vmin=vmin, *args, **kwargs) else: bins = kwargs.pop('bins', 10) density = kwargs.pop('density', False) cmin = kwargs.pop('cmin', None) cmax = kwargs.pop('cmax', None) pdf, x, y = np.histogram2d(data_x, data_y, bins, rge, density, weights) levels = iso_probability_contours(pdf, levels) pdf = np.digitize(pdf, levels, right=True) pdf = np.array(levels)[pdf] pdf = np.ma.masked_array(pdf, pdf < levels[1]) if cmin is not None: pdf[pdf < cmin] = np.ma.masked if cmax is not None: pdf[pdf > cmax] = np.ma.masked image = ax.pcolormesh(x, y, pdf.T, cmap=cmap, vmin=vmin, *args, **kwargs) ax.patches += [plt.Rectangle((0, 0), 0, 0, fc=cmap(0.999), ec=cmap(0.32), lw=2, label=label)] ax.set_xlim(*check_bounds(x, xmin, xmax), auto=True) ax.set_ylim(*check_bounds(y, ymin, ymax), auto=True) return image
def kde_plot_1d(ax, data, *args, **kwargs): """Plot a 1d marginalised distribution. This functions as a wrapper around matplotlib.axes.Axes.plot, with a kernel density estimation computation provided by scipy.stats.gaussian_kde in between. All remaining keyword arguments are passed onwards. Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on. data: np.array Samples to generate kernel density estimator. weights: np.array, optional Sample weights. ncompress: int, optional Degree of compression. Default 1000 xmin, xmax: float lower/upper prior bound. optional, default None levels: list values at which to draw iso-probability lines. optional, default [0.95, 0.68] facecolor: bool or string If set to True then the 1d plot will be shaded with the value of the ``color`` kwarg. Set to a string such as 'blue', 'k', 'r', 'C1' ect. to define the color of the shading directly. optional, default False Returns ------- lines: matplotlib.lines.Line2D A list of line objects representing the plotted data (same as matplotlib matplotlib.axes.Axes.plot command) """ if len(data) == 0: return np.zeros(0), np.zeros(0) if data.max()-data.min() <= 0: return kwargs = normalize_kwargs( kwargs, dict(linewidth=['lw'], linestyle=['ls'], color=['c'], facecolor=['fc'], edgecolor=['ec'])) levels = kwargs.pop('levels', [0.95, 0.68]) xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) weights = kwargs.pop('weights', None) ncompress = kwargs.pop('ncompress', 1000) density = kwargs.pop('density', False) cmap = kwargs.pop('cmap', None) color = kwargs.pop('color', (next(ax._get_lines.prop_cycler)['color'] if cmap is None else cmap(0.68))) facecolor = kwargs.pop('facecolor', False) if 'edgecolor' in kwargs: edgecolor = kwargs.pop('edgecolor') if edgecolor: color = edgecolor else: edgecolor = color q = kwargs.pop('q', '5sigma') q = quantile_plot_interval(q=q) if weights is not None: data = data[weights != 0] weights = weights[weights != 0] x, w = sample_compression_1d(data, weights, ncompress) kde = gaussian_kde(x, weights=w) p = kde(x) p /= p.max() i = ((x > quantile(x, q[0], w)) & (x < quantile(x, q[1], w))) if xmin is not None: i = i & (x > xmin) if xmax is not None: i = i & (x < xmax) sigma = np.sqrt(kde.covariance[0, 0]) pp = cut_and_normalise_gaussian(x[i], p[i], sigma, xmin, xmax) pp /= pp.max() area = np.trapz(x=x[i], y=pp) if density else 1 ans = ax.plot(x[i], pp/area, color=color, *args, **kwargs) ax.set_xlim(*check_bounds(x[i], xmin, xmax), auto=True) if facecolor and facecolor not in [None, 'None', 'none']: if facecolor is True: facecolor = color c = iso_probability_contours_from_samples(pp, contours=levels, weights=w) cmap = basic_cmap(facecolor) fill = [] for j in range(len(c)-1): fill.append(ax.fill_between(x[i], pp, where=pp >= c[j], color=cmap(c[j]), edgecolor=edgecolor)) return ans, fill return ans
def fastkde_plot_1d(ax, data, *args, **kwargs): """Plot a 1d marginalised distribution. This functions as a wrapper around matplotlib.axes.Axes.plot, with a kernel density estimation computation provided by the package fastkde in between. All remaining keyword arguments are passed onwards. Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on data: np.array Uniformly weighted samples to generate kernel density estimator. xmin, xmax: float lower/upper prior bound optional, default None levels: list values at which to draw iso-probability lines. optional, default [0.95, 0.68] facecolor: bool or string If set to True then the 1d plot will be shaded with the value of the ``color`` kwarg. Set to a string such as 'blue', 'k', 'r', 'C1' ect. to define the color of the shading directly. optional, default False Returns ------- lines: matplotlib.lines.Line2D A list of line objects representing the plotted data (same as matplotlib matplotlib.axes.Axes.plot command) """ kwargs = normalize_kwargs( kwargs, dict(linewidth=['lw'], linestyle=['ls'], color=['c'], facecolor=['fc'], edgecolor=['ec'])) if len(data) == 0: return np.zeros(0), np.zeros(0) if data.max()-data.min() <= 0: return levels = kwargs.pop('levels', [0.95, 0.68]) xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) density = kwargs.pop('density', False) cmap = kwargs.pop('cmap', None) color = kwargs.pop('color', (next(ax._get_lines.prop_cycler)['color'] if cmap is None else cmap(0.68))) facecolor = kwargs.pop('facecolor', False) if 'edgecolor' in kwargs: edgecolor = kwargs.pop('edgecolor') if edgecolor: color = edgecolor else: edgecolor = color q = kwargs.pop('q', '5sigma') q = quantile_plot_interval(q=q) try: x, p, xmin, xmax = fastkde_1d(data, xmin, xmax) except NameError: raise ImportError("You need to install fastkde to use fastkde") p /= p.max() i = ((x > quantile(x, q[0], p)) & (x < quantile(x, q[1], p))) area = np.trapz(x=x[i], y=p[i]) if density else 1 ans = ax.plot(x[i], p[i]/area, color=color, *args, **kwargs) ax.set_xlim(xmin, xmax, auto=True) if facecolor and facecolor not in [None, 'None', 'none']: if facecolor is True: facecolor = color c = iso_probability_contours(p[i], contours=levels) cmap = basic_cmap(facecolor) fill = [] for j in range(len(c)-1): fill.append(ax.fill_between(x[i], p[i], where=p[i] >= c[j], color=cmap(c[j]), edgecolor=edgecolor)) return ans, fill return ans
def quantile(self, q=0.5, numeric_only=True, interpolation='linear'): """Weighted quantile of the sampled distribution.""" if not numeric_only: raise NotImplementedError("numeric_only kwarg not implemented") return quantile(self.values, q, self.weights, interpolation)
def quantile(self, q=0.5): """Weighted quantile of the sampled distribution.""" return quantile(self.values, q, self.weights)
def kde_plot_1d(ax, data, *args, **kwargs): """Plot a 1d marginalised distribution. This functions as a wrapper around matplotlib.axes.Axes.plot, with a kernel density estimation computation provided by scipy.stats.gaussian_kde in between. All remaining keyword arguments are passed onwards. Parameters ---------- ax: matplotlib.axes.Axes axis object to plot on. data: np.array Samples to generate kernel density estimator. weights: np.array, optional Sample weights. ncompress: int, optional Degree of compression. Default 1000 xmin, xmax: float lower/upper prior bound. optional, default None Returns ------- lines: matplotlib.lines.Line2D A list of line objects representing the plotted data (same as matplotlib matplotlib.axes.Axes.plot command) """ if len(data) == 0: return np.zeros(0), np.zeros(0) if data.max() - data.min() <= 0: return kwargs = normalize_kwargs(kwargs, dict(linewidth=['lw'], linestyle=['ls'], color=['c']), drop=['fc', 'ec']) xmin = kwargs.pop('xmin', None) xmax = kwargs.pop('xmax', None) weights = kwargs.pop('weights', None) ncompress = kwargs.pop('ncompress', 1000) cmap = kwargs.pop('cmap', None) color = kwargs.pop('color', (next(ax._get_lines.prop_cycler)['color'] if cmap is None else cmap(0.68))) q = kwargs.pop('q', '5sigma') q = quantile_plot_interval(q=q) if weights is not None: data = data[weights != 0] weights = weights[weights != 0] x, w = sample_compression_1d(data, weights, ncompress) kde = gaussian_kde(x, weights=w) p = kde(x) p /= p.max() i = ((x > quantile(x, q[0], w)) & (x < quantile(x, q[1], w))) if xmin is not None: i = i & (x > xmin) if xmax is not None: i = i & (x < xmax) sigma = np.sqrt(kde.covariance[0, 0]) pp = cut_and_normalise_gaussian(x[i], p[i], sigma, xmin, xmax) pp /= pp.max() ans = ax.plot(x[i], pp, color=color, *args, **kwargs) ax.set_xlim(*check_bounds(x[i], xmin, xmax), auto=True) return ans